Daffodil-Because the medigun auto aims and the crossbow doesn't. Also you sacrifice heals/minute if you miss, situational awareness while arrowing people, scout speed if you had a beam on a scout, and potentially your uber (or uber targets) if you switch away from your medigun.
You make it sound a bit punishing for using arrows, but since the crossbow shoots relatively fast and has a passive reload, to me this sacrifice seems worth it really.
Heals/minute don't matter that much.
Situational awareness doesn't seem relevant that often since most of the time you arrow from a spot where you can shoot safely. The chance that you will know more of what's around you when you're just beaming instead of arrowing is pretty small. We're also talking about close range here.
You lose speed that you could've had by not healing a scout, but perhaps that makes the scout more vulnerable because an arrow would've just healed him instantly. Again, an arrow shoots pretty quick so you don't even lose much time/distance. This part is very situational though.
If you sacrifice uber by using arrows then that's your own mistake really. When you're in an uber (or just about to) you shouldn't really be arrowing teammates. Unless you want to heal them up very quick right before the push.
This is just how I experienced it and think about it and I'm not questioning your statement. The things you named just don't seem that important to me, but I'm curious why you think they are ^^